I keep getting messages from Galaxy about my Quake 1 saves being too big. Is there an issue with the in-game downloadable add-ons (Honey, etc.) being counted towards GOGs save-data size quotient?
Am I missing something else?

Any help would be greatly appreciated.

Yes that's exactly the problem and there seems to be no working solution so far. It's annoying.

Current workaround:

1. Check sync cloud saves is ON for Quake 1 Enchanced (right-click box art -> Manage Installation -> Configure -> Features -> tick Sync local saves with Galaxy cloud).
2. Launch Quake 1 Enhanced through Galaxy.
3. In-game - navigate to Add-ons.
4. Delete each add-on, may have to back out of add-on menu and re-enter to check they have been removed.
5. Quit Quake 1 Enhanced.
6. Wait for Galaxy to sync saves.
7. Turn cloud saves OFF for Quake 1 Enchanced (right-click box art -> Manage Installation -> Configure -> Features -> untick Sync local saves with Galaxy cloud).
8. Launch Quake 1 Enhanced through Galaxy.
9. Navigate to and download Add-Ons as required.